http://lod.bco-dmo.org/id/dataset/879120
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2022-08-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Body length, right postoral rod length, and stomach length of Dendraster excentricus and Lytechinus pictus larvae raised at three culture densities on two food rations from 2021-2022 (LIPs on Larval Feeding project)
2022-08-24
publication
2022-08-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-09-26
publication
https://doi.org/10.26008/1912/bco-dmo.879120.1
Bruno Pernet
California State University Long Beach
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Pernet, B. (2022) Body length, right postoral rod length, and stomach length of Dendraster excentricus and Lytechinus pictus larvae raised at three culture densities on two food rations from 2021-2022 (LIPs on Larval Feeding project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-08-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.879120.1 [access date]
Body length, right postoral rod length, and stomach length of Dendraster excentricus and Lytechinus pictus larvae raised at three culture densities on two food rations. Dataset Description: Methods and Sampling: <p><strong>Methodology: </strong></p>
<p>Detailed methods are presented in a manuscript in press at Marine Ecology Progress Series as of 27 June 2022 (Nilsson &amp; Pernet (2022). A brief summary of the larval culture and counting methods are presented below.</p>
<p>Adult echinoids (<em>Dendraster excentricus </em>and <em>Lytechinus pictus</em>) were collected from two sites near San Pedro, California and spawned in lab to yield three full-sibling families per experiment. In each experiment, blastulae were allowed to develop for one day, then distributed to beakers. Ten beakers were prepared for each of three culture density treatments (0.015, 0.05, and 0.25 larvae ml<sup>-1</sup>). Half (five) of these beakers were allocated a daily ration of <em>Rhodomonas lens </em>(CCMP739) at concentrations of 250 cells ml<sup>-1</sup> and the other half (five) allocated 5,000 cells ml<sup>-1</sup> to establish two food ration treatments; all received daily water changes.</p>
<p>In each experiment, we assessed the accuracy of larval aliquoting by preparing three additional count control beakers for the 0.05 and 0.25 larvae ml<sup>-1</sup> treatments as described above. Larvae in these beakers were fed the higher (5,000 cells ml<sup>-1</sup>) food ration and cultured at room temperature to accelerate their development, increasing their size and opacity and making them easier to count accurately. At 3 days post fertilization (dpf), the larvae in each count control beaker were concentrated into a small (5 – 20 ml) volume and killed with ethanol. They were then counted to estimate the actual number of blastulae that had been delivered to the experimental beakers at each density. No count control beakers were prepared for the 0.015 larvae ml<sup>-1</sup> treatment because those beakers were populated by counting out and pipetting the exact number of desired larvae (15) to each beaker.</p>
<p>&nbsp;</p>
<p><strong>Sampling:</strong></p>
<p>The mean larval count for each treatment was compared to the expected number of larvae; as all beakers contained 1000 ml, the expected numbers were 50 and 250 for the 0.05 and 0.25 larvae ml<sup>-1</sup> treatments respectively.</p>
<p>These larval counts can be found attached to this metadata record below Data Files within the file, larvae_density_counts.csv.</p>
<p>&nbsp;</p>
<p><strong>Analysis:</strong></p>
<p>This analysis was reproduced from Nilsson &amp; Pernet (2022). Studies on feeding structure plasticity in echinoids use diverse statistical approaches in their analyses (McAlister &amp; Miner 2018), a fact that exacerbates the difficulty of comparing results among studies which are already diverse in experimental technique. To enable straightforward comparison with the results of Kacenas &amp; Podolsky (2018), we used the same statistical approach that they did, creating linear mixed-effects models for both dependent variables (PORL and SL) for each experiment. Kacenas &amp; Podolsky (2018) did this using IBM SPSS 24 (IBM Corp. 2016), but we did our analyses in R 4.1.0 (R Core Team 2021) using the lmer function provided by the lme4 1.1-27 package (Bates et al. 2015) and extended by the lmerTest 3.1-3 package (Kuznetsova et al. 2017). Food ration and larval density were treated as fixed effects, beaker as a random effect, body length as a covariate, and either postoral rod length or stomach length as response variables. Estimated marginal means were calculated in R using the emmeans package (Lenth 2021) and compared using the glht function of the multcomp package (Hothorn et al. 2008). To verify that any differences in results were not due to differences between software packages in the implementation of statistical routines, we also analyzed the data from <em>D. excentricus</em> Expt 1 using IBM SPSS 24 (IBM Corp. 2016). Similar values were produced by both packages.</p>
<p>To ensure our statistical conclusions were not particular to the approach that both we and Kacenas &amp; Podolsky (2018) used, we conducted several additional analyses, including similar linear mixed-effects models that included covariate interaction terms as well as a simpler approach using ANOVA to compare PORL and SL adjusted for larval size by dividing each by BL. These analyses, which are detailed in the Supplementary Material, all produced results similar to those of our primary analysis (Tables S1-S5, Fig. S1).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756531 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756531
completed
Bruno Pernet
California State University Long Beach
562-985-5378
Biological Sciences, CSU Long Beach 1250 Bellflower Blvd.
Long Beach
CA
90840
USA
bruno.pernet@csulb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Spawn_date
Species
Experiment
Beaker
Culture_density
Food
Right_PO_arm_length
Stomach_length
Midline_body_length
Age
Stage
Image
QlClick Camera (Teledyne Photometrics)
BD Accuri C6 Flow Cytometer (BD Biosciences)
Olympus BX-51 Compound Microscope (Olympus Scientific Solutions)
theme
None, User defined
date
species scientific name (binomial)
experiment id
No BCO-DMO term
density
treatment
length
age
stage
file_name
featureType
BCO-DMO Standard Parameters
Camera
Flow Cytometer
Microscope - Optical
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
RUI: Effects of large inedible particles on larval feeding, planktonic larval duration, and juvenile quality in marine invertebrates
https://osprey.bco-dmo.org/project/727167
RUI: Effects of large inedible particles on larval feeding, planktonic larval duration, and juvenile quality in marine invertebrates
<p><em>NSF award abstract:</em><br />
Many ecologically and economically important marine invertebrates (e.g., oysters, crabs, and sea urchins) have life cycles that include feeding larval stages that live drifting in the water as part of the plankton. These larvae spend days or weeks feeding on tiny algal particles to fuel their development until they can metamorphose into juveniles. In nature, however, the plankton includes not only edible particles, but also many particles that are too large to be eaten but which may interfere with feeding on edible particles. These include, for example, large algal particles, eggs and embryos of other invertebrates, re-suspended sediment, and anthropogenic nano- and micro-plastics. When larvae encounter large inedible particles, they may respond by altering their swimming behavior to avoid them, or by capturing and then rejecting them. Such interactions reduce the rate at which larvae can capture edible particles, which forces them to either spend more time feeding before metamorphosis (increasing their overall risk of dying due to planktonic predators), or to metamorphose with less energy, producing juveniles in relatively poor condition. This project examines how large inedible particles affect feeding, time to metamorphosis, and juvenile condition in the larvae of diverse marine invertebrates. The project has the potential to dramatically change our understanding of how larvae feed and survive in natural communities, and thus our understanding of the population dynamics of these important organisms. The project will support research training opportunities for undergraduate and graduate students at California State University Long Beach, a primarily undergraduate institution, as well as summer research internships for students at two local community colleges. Project data will be integrated into laboratory modules in undergraduate courses. Finally, data on the reproductive biology of diverse California marine invertebrates will be added to a public website that is widely used by members of the public, students, and biologists interested in the development, life histories, ecology, and evolution of these common animals.</p>
<p>The factors that control planktonic duration and juvenile condition in marine invertebrates with feeding larvae have long been recognized as critical to understanding their ecology and evolution. Larval feeding environment is clearly one of those factors, but previous work has focused almost exclusively on one feature of that environment, the abundance of food. This project will evaluate the importance of another potentially critical dimension of the larval feeding environment: the presence of large inedible particles, which are frequently abundant in natural plankonic communities. It takes a comparative approach to address two key questions about the effects of large inedible particles on larvae (including those of echinoderms, annelids, and molluscs) that feed using several different particle capture mechanisms. First, do large inedible particles present in natural plankton reduce larval feeding rates? And second, does the presence of large inedible particles extend larval planktonic duration or result in the production of lower quality juveniles? Feeding rates of larvae will be measured in short-term experiments in which larvae are exposed to both food and to natural or artificial large inedible particles over a range of concentrations. Effects of large inedible particles on planktonic duration and juvenile quality will be measured by culturing larvae through their entire life cycles in the presence of large inedible particles at various concentrations. Because feeding performance is an important determinant of planktonic duration, larval survival, and juvenile condition, the project will add greatly to our understanding of how conditions in the plankton affect the population dynamics of the many marine invertebrates with feeding larvae.</p>
LIPs on Larval Feeding
largerWorkCitation
project
eng; USA
oceans
2021-01-01
2022-04-30
Southern California Bight
0
BCO-DMO catalogue of parameters from Body length, right postoral rod length, and stomach length of Dendraster excentricus and Lytechinus pictus larvae raised at three culture densities on two food rations from 2021-2022 (LIPs on Larval Feeding project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/881040.rdf
Name: Spawn_date
Units: unitless
Description: <p>Date (year-month-day) larvae were spawned.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881041.rdf
Name: Species
Units: unitless
Description: <p>Species of larva.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881042.rdf
Name: Experiment
Units: unitless
Description: <p>Short name of experiment to which larva belonged.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881043.rdf
Name: Beaker
Units: unitless
Description: <p>Name of beaker; unique within experiment but not across experiments.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881044.rdf
Name: Culture_density
Units: ml-1
Description: <p>Nominal concentration of larvae.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881045.rdf
Name: Food
Units: ml-1
Description: <p>Nominal concentration of Rhodomonas lens cells.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881046.rdf
Name: Right_PO_arm_length
Units: um
Description: <p>Length of the right postoral arm; measured from tip to the junction of the postoral rod with the transverse rod.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881047.rdf
Name: Stomach_length
Units: um
Description: <p>Length of the stomach along the body midline.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881048.rdf
Name: Midline_body_length
Units: um
Description: <p>Length of the larva along the body midline.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881049.rdf
Name: Age
Units: days
Description: <p>Approximate age at which larvae were photographed.</p>
http://lod.bco-dmo.org/id/dataset-parameter/881050.rdf
Name: Stage
Units: unitless
Description: <p>Stage of larval development; either four-arm (postoral and anterolateral arms only) or six-arm (postoral, anterolateral, and posterodorsal arms).</p>
http://lod.bco-dmo.org/id/dataset-parameter/881051.rdf
Name: Image
Units: unitless
Description: <p>Name of image file from which measurements were derived.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
618
https://darchive.mblwhoilibrary.org/bitstream/1912/29371/1/parameters_larvae_density_counts.csv
download
404126924
https://darchive.mblwhoilibrary.org/bitstream/1912/29371/2/larval_images_Peter_Nilsson.zip
download
1868
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/710a2b6b-fa80-5b51-b68c-182901980874/content
download
68916
https://darchive.mblwhoilibrary.org/bitstream/1912/29371/4/dataset-879120_larvae-density-morphometrics__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.879120.1
download
onLine
dataset
<p><strong>Methodology: </strong></p>
<p>Detailed methods are presented in a manuscript in press at Marine Ecology Progress Series as of 27 June 2022 (Nilsson &amp; Pernet (2022). A brief summary of the larval culture and counting methods are presented below.</p>
<p>Adult echinoids (<em>Dendraster excentricus </em>and <em>Lytechinus pictus</em>) were collected from two sites near San Pedro, California and spawned in lab to yield three full-sibling families per experiment. In each experiment, blastulae were allowed to develop for one day, then distributed to beakers. Ten beakers were prepared for each of three culture density treatments (0.015, 0.05, and 0.25 larvae ml<sup>-1</sup>). Half (five) of these beakers were allocated a daily ration of <em>Rhodomonas lens </em>(CCMP739) at concentrations of 250 cells ml<sup>-1</sup> and the other half (five) allocated 5,000 cells ml<sup>-1</sup> to establish two food ration treatments; all received daily water changes.</p>
<p>In each experiment, we assessed the accuracy of larval aliquoting by preparing three additional count control beakers for the 0.05 and 0.25 larvae ml<sup>-1</sup> treatments as described above. Larvae in these beakers were fed the higher (5,000 cells ml<sup>-1</sup>) food ration and cultured at room temperature to accelerate their development, increasing their size and opacity and making them easier to count accurately. At 3 days post fertilization (dpf), the larvae in each count control beaker were concentrated into a small (5 – 20 ml) volume and killed with ethanol. They were then counted to estimate the actual number of blastulae that had been delivered to the experimental beakers at each density. No count control beakers were prepared for the 0.015 larvae ml<sup>-1</sup> treatment because those beakers were populated by counting out and pipetting the exact number of desired larvae (15) to each beaker.</p>
<p>&nbsp;</p>
<p><strong>Sampling:</strong></p>
<p>The mean larval count for each treatment was compared to the expected number of larvae; as all beakers contained 1000 ml, the expected numbers were 50 and 250 for the 0.05 and 0.25 larvae ml<sup>-1</sup> treatments respectively.</p>
<p>These larval counts can be found attached to this metadata record below Data Files within the file, larvae_density_counts.csv.</p>
<p>&nbsp;</p>
<p><strong>Analysis:</strong></p>
<p>This analysis was reproduced from Nilsson &amp; Pernet (2022). Studies on feeding structure plasticity in echinoids use diverse statistical approaches in their analyses (McAlister &amp; Miner 2018), a fact that exacerbates the difficulty of comparing results among studies which are already diverse in experimental technique. To enable straightforward comparison with the results of Kacenas &amp; Podolsky (2018), we used the same statistical approach that they did, creating linear mixed-effects models for both dependent variables (PORL and SL) for each experiment. Kacenas &amp; Podolsky (2018) did this using IBM SPSS 24 (IBM Corp. 2016), but we did our analyses in R 4.1.0 (R Core Team 2021) using the lmer function provided by the lme4 1.1-27 package (Bates et al. 2015) and extended by the lmerTest 3.1-3 package (Kuznetsova et al. 2017). Food ration and larval density were treated as fixed effects, beaker as a random effect, body length as a covariate, and either postoral rod length or stomach length as response variables. Estimated marginal means were calculated in R using the emmeans package (Lenth 2021) and compared using the glht function of the multcomp package (Hothorn et al. 2008). To verify that any differences in results were not due to differences between software packages in the implementation of statistical routines, we also analyzed the data from <em>D. excentricus</em> Expt 1 using IBM SPSS 24 (IBM Corp. 2016). Similar values were produced by both packages.</p>
<p>To ensure our statistical conclusions were not particular to the approach that both we and Kacenas &amp; Podolsky (2018) used, we conducted several additional analyses, including similar linear mixed-effects models that included covariate interaction terms as well as a simpler approach using ANOVA to compare PORL and SL adjusted for larval size by dividing each by BL. These analyses, which are detailed in the Supplementary Material, all produced results similar to those of our primary analysis (Tables S1-S5, Fig. S1).</p>
Specified by the Principal Investigator(s)
<p><strong>Processing notes from Researcher:&nbsp;</strong></p>
<p>The morphometric data (Midline_body_length, Right_PO_arm_length and Stomach_length) were measured with the Fiji distribution (2.3.0/1.53f51) of ImageJ (Schindelin et al. 2012). The exact landmarks used to define these measurements are presented in Figure 1 of Nilsson &amp; Pernet (2022). These data were subsequently analyzed as described in Nilsson &amp; Pernet (2022).</p>
<p>The code required to reproduce these analyses is available at https://doi.org/10.5281/zenodo.6824313.</p>
<p>&nbsp;</p>
<p><strong>Problems/Issues Notes from Researcher</strong></p>
<p>For the second experiment on Dendraster excentricus (“D. excentricus Expt 1”), the count control beakers for both the 0.05 and 0.25 ml-1 larval densities yielded approximately half the expected number of larvae; we view this as a conservative error, providing a stronger test of the ability of larvae to exhibit plasticity at low culture densities than the intended concentrations. As we hand-counted into the 0.015 larvae ml-1 treatments, those treatments could not have been affected by inaccuracies in aliquoting. See the associated density_counts dataset for details.</p>
<p>For the 0.015 larvae ml-1 density treatment in both Lytechinus pictus experiments (“L. pictus Expt 1” and “L. pictus Expt 2”), there were often fewer than five larvae that could be measured, due to a combination of low survival and high incidence of larvae with missing or obviously broken right postoral rods. Low survival and abnormal arm morphology past 5 dpf was also noted in a study on culture methods for larvae of the congener Lytechinus variegatus (Buitrago et al. 2005), which are known to be particularly fragile and thus likely to be damaged during water changes (Lowe &amp; Wray 2000).</p>
<p>Note that the lowest culture density treatment (0.015 larvae ml-1) was only introduced beginning in the second experiment, and thus was not present in D. excentricus Expt 1.&nbsp;</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
QlClick Camera (Teledyne Photometrics)
QlClick Camera (Teledyne Photometrics)
PI Supplied Instrument Name: QlClick Camera (Teledyne Photometrics) PI Supplied Instrument Description:At set points in the experiments (5 or 7 days), larvae were photographed in dorsal view with a QIClick camera (Teledyne Photometrics) mounted on an Olympus BX-51 compound microscope (Olympus Scientific Solutions) using a 10x (D. excentricus) or 20x (L. pictus) objective. The Fiji distribution of ImageJ (Schindelin et al. 2012) was used to measure the lengths of the right postoral rod, stomach, and body of each photographed larva. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
BD Accuri C6 Flow Cytometer (BD Biosciences)
BD Accuri C6 Flow Cytometer (BD Biosciences)
PI Supplied Instrument Name: BD Accuri C6 Flow Cytometer (BD Biosciences) PI Supplied Instrument Description:A BD Accuri C6 Flow Cytometer (BD Biosciences), was used to determine the concentration of Rhodomonas lens. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Olympus BX-51 Compound Microscope (Olympus Scientific Solutions)
Olympus BX-51 Compound Microscope (Olympus Scientific Solutions)
PI Supplied Instrument Name: Olympus BX-51 Compound Microscope (Olympus Scientific Solutions) PI Supplied Instrument Description:At a set point in the experiments (5 or 7 days) larvae were photographed in dorsal view with a QIClick camera (Teledyne Photometrics) mounted on an Olympus BX-51 compound microscope (Olympus Scientific Solutions) using a 10x (D. excentricus) or 20x (L. pictus) objective. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/